Britain's intelligence agencies were surprised by the Arab spring, and their failure to realise unrest would spread so rapidly may reveal a lack of understanding of the region, according to the parliamentary body set up to scrutinise their activities.

A particularly sharp passage of the intelligence and security committee's (ISC) report describes as "ill-considered" an attempt by MI6 to smuggle into Libya two officers who were promptly seized by rebels.

The report says that at the time the Arab spring erupted, both MI6 and GCHQ, the government's electronic eavesdropping centre, were cutting resources devoted to Arab countries.

The criticism of MI6's attitude is all the more significant given the agency's traditional close ties with the Arab world.

The ISC, chaired by the former Conservative foreign secretary Sir Malcolm Rifkind, said it was understandable that the intelligence agencies were taken by surprise, "as indeed were the governments in the countries affected".

However, it said there were questions about whether the agencies "should have been able to anticipate how events might subsequently unfold, and whether the fact that they did not realise that the unrest would spread so rapidly across the Arab world demonstrates a lack of understanding about the region".

SAS troops escorted MI6 officers to Libya in a Chinook helicopter and dropped them off at a desert location south of Benghazi in the middle of the night in March 2011. The mission was an embarrassment to the British government and the anti-Gaddafi rebels alike. MI6 "misjudged the nature and level of risk involved", the ISC said.

It noted that the lessons had been taken seriously by MI6, and added: "We would have expected nothing less." The incident "demonstrates a lack of operational planning that we would not have expected from [MI6]and other participants", it said.

Cuts being made in Whitehall's defence intelligence staff mean greater risks would have to be taken "when reacting to the next crisis than was the case with the Libya campaign", the ISC warned. It said GCHQ's difficulties in retaining internet and cyber specialists attracted by higher salaries in the private sector was a matter of grave concern.

The report said Jonathan Evans, head of MI5, had told the ISC there had been "very considerable erosion of al-Qaida's senior leadership capability in Pakistan, and to some extent now in Yemen, as a result of drone strikes".

Al-Qaida had to spend a lot of its time trying to protect itself, Evans was quoted as saying. "It is much more difficult to take action if you are permanently in fear that you are going to be attacked. I think that has had a strategic impact on al-Qaida's senior leadership."

The ISC said British intelligence agencies were now concerned that al-Qaida in Iraq "may gain a lasting foothold in Syria if there is a prolonged power vacuum, and also at the prospect of Syrian conventional and chemical weapons stockpiles falling into the hands of terrorist groups".

The MPs and peers on the ISC avoid criticising MI6 for its involvement in the abduction of Libyan dissidents to Gaddafi's secret police in 2004 or in the abuse of terror suspects by the CIA. "To protect the UK our agencies must work with foreign agencies, some of whom do not meet our standards. In so doing, there is a risk that our agencies will, indirectly and inadvertently, be linked to such activities. It is unfortunate, but inescapable, that those risks cannot always be wholly eliminated," the report said.

The government's decision to abandon control orders for terrorism suspects and replace them with terrorism prevention and investigation measures potentially increased the threat from terrorists, the ISC said.